Summary: Putative viral replication protein
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Putative viral replication protein Provide feedback
This is a family of viral ORFs from various plant and animal ssDNA circoviruses. Published evidence to support the annotated function "viral replication associated protein" has not be found.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR003365
Proteins in this entry are essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication introducing an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3'. This initiates rolling circle replication (RCR). Following cleavage, the protein binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|
|nucleotidyltransferase activity (GO:0016779)|
|ATPase activity, uncoupled (GO:0042624)|
|Biological process||DNA replication (GO:0006260)|
|protein-DNA covalent cross-linking (GO:0018142)|
- the number of sequences which exhibit this architecture
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This clan includes replication proteins for viruses and plasmids. This domain is known to bind DNA. The members of this clan have three motifs. The central HXH is conserved in most families in the clan.
The clan contains the following 9 members:DUF1424 Gemini_AL1 Mob_Pre MobA_MobL Phage_GPA Relaxase Rep_1 T_Ag_DNA_bind Viral_Rep
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Seed source:||Pfam-B_1223 (release 5.2)|
|Author:||Bashton M, Bateman A|
|Number in seed:||19|
|Number in full:||1309|
|Average length of the domain:||77.10 aa|
|Average identity of full alignment:||47 %|
|Average coverage of the sequence by the domain:||29.31 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Viral_Rep domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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